From a service standpoint, the route down the San Joaquin Valley is certainly the way to go. Far more on-line business there than on the coast though the temptation for a stop every 20 miles must be resisted (leave conventional Amtrak to cover that). There must be a stop in Fresno. There should be stops in Bakersfield and (if it doesn't veer off and head for Los Banos and Pacheco Pass) Merced and Stockton (min. 60, preferably 100 miles apart) on the way to Sac. Also, even with a Tehachapi-Palmdale compromise for the LA approach it's far shorter than a coast run -- you *could* do it now (if UP/BNSF had track space over Tehachapi) without violating speed limits in about 12 hours Oakland-LA vs. 14 when you're lucky down the coast.

I see no reason to follow the Santa Fe south of Fresno, though. If UP won't let HSR follow their line, put it on the other side of the freeway on new r/w. Shorter distance to Bakersfield and there's really no need for a HSR stop at Hwy 198 (Hanford or Visalia) - existing Amtrak service should be used for that. In fact, the route should favor sharing with freeways rather than with UP or BNSF in general. Read "Ecotopia" for the concept.

It would be lovely, if there were unlimited cash, to punch straight through the mountains from Bakersfield to LA. Unlimited cash is not available. So I reluctantly agree with the decision by HSR to use Tehachapi and Palmdale (then paralleling Metrolink) to enter LA. Even though it's longer than a straight-through punch, it's less expensive to build and maintain (and more fixable after the inevitable earthquakes). The online business at Palmdale (station at the airport please!) is a plus, though not a major one (other than politically).

I'm agnostic on routes into the Bay Area. Both proposals that have traction (Pacheco and Altamont) have pluses and minuses. Pacheco has the major plus of avoiding seriously built-up areas until it gets almost into San Jose (less noise/NIMBYs) and has the potential for serving the San Jose airport, but does have other issues. Altamont has more potential for on-line business, but far more NIMBYs. Once it gets close to town, though, it should just drop onto electrified standard tracks (fully grade-separated of course) and operate into whatever station makes sense at 125 tops. Ditto at the LA end -- improve Metrolink to allow 90 with conventional trains and 125 or so with HSR (i.e. no more grade crossings) and you can get from Palmdale to LAUS with HSR in an hour (vs current almost 2). The prototype is most of the NE Corridor.

A setup like that would nearly duplicate how most of the Euro systems worked when started: high speed in the country for the long-distance run, and share improved conventional tracks in the terminal areas. Something like that might actually be buildable for the money HSR is currently talking about over the next 20 years, and would be far better than what's being talked about most other places in the US though barely competitive on a world scale. It would allow expresses SF/LA in 3 hr or less (stop only in Fresno) and locals in 4 or so. Yes, it's not the 2-hour train that was advertised when the bonds were sold, but that was always a pipe dream -- even shooting down I-5 nonstop and straight thru the mountains at 200+ would barely make it, and couldn't come near generating the revenue needed just to cover operating costs. And the revenue thing is important; to get private interest (not just pay Amtrak to run it) there has to be some prospect of profit, whether from the passengers themselves or from them covering their basic cost then hauling some overnight freight (Mixed Train Nightly!).